The alignment of the atoms are 1-2-3-4 and 2-3-4 are almost in a straight
line. I was aware that the dihedral angle is not defined actually. But,
the force constant was set zero so I wanted it to be zero rather than nan.
Sander definitely gives a finite dihedral energy.
In my specific case, uu = uv = 0.
On Thu, Jul 29, 2010 at 10:17 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Jul 29, 2010, InSuk Joung wrote:
> >
> > Recently I posted a problem about the calculation of dihedral energy
> using
> > NAB to AMBER mailing list. I think I found the source of the problem
> >
> > At the 458th line of eff.c:
> >
> > uu = (aa * bb) - (ab * ab);
> > vv = (bb * cc) - (bc * bc);
> > uv = (ab * bc) - (ac * bb);
> > den = 1.0 / sqrt(uu * vv);
> > co = uv * den;
> >
> > When 'uu' or 'vv' is 0. 'den' goes to infinity, which causes a problem.
> I
> > am not sure if this way to calculate the dihedral angle is
> computationally
> > efficient but I believe dihedral angles can be calculated using atan2
> > without the numerical problem. Can anybody suggest a detour for this?
>
> First, what is the geometry of the four atoms you are using here? Is
> either
> the 1-2-3 or the 2-3-4 angle 180 degrees? (Dihedral torsions are not well
> defined in such cases).
>
> Second, when uu or vv are zero, is uv also zero?
>
> ....dac
>
>
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>
--
Best,
InSuk Joung
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Received on Thu Jul 29 2010 - 20:00:03 PDT
